Preprocess data for plotting in the dashboard

library(glue)

Attaching package: 㤼㸱glue㤼㸲

The following object is masked from 㤼㸱package:dplyr㤼㸲:

    collapse

There were 16 warnings (use warnings() to see them)

Define common columns

cols <- c(
  "Date",
  "Regio",
  "Period",
  "Interval",
  "Population",
  "Deaths",
  "MortalityRate")

Load historical data for flu dataset

cols.historic <-

Warning messages:
1: In readChar(file, size, TRUE) : truncating string with embedded nuls
2: In readChar(file, size, TRUE) : truncating string with embedded nuls
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  c(
    cols,
    "Year"
  )

data.historic <- union_all(
  read_rds("../results/data.Rds") %>% select(cols.historic),
  read_rds("../results/data.spatial.Rds") %>% select(cols.historic, "RegioS") %>% mutate("Regio" = RegioS) %>% select(-"RegioS"),
)

Note: Using an external vector in selections is ambiguous.
i Use `all_of(cols.historic)` instead of `cols.historic` to silence this message.
i See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
This message is displayed once per session.

# data.flu2018 <- data.historic %>% 
#   filter(Year == 2018 | Year == 2017) %>% 
#   group_by(Year) %>%
#   mutate(
#     LastPeriod = max(Period, na.rm = T),
#     Period = if_else(Year == 2017 & Period == LastPeriod, 0, Period),
#   ) %>%
#   ungroup() %>%
#   mutate(Year = if_else(Period == 0, 2018, Year)) %>%
#   filter(Year == 2018) %>%
#   rename(Flu2018 = MortalityRate)

Additional RIVM data

Warning in readChar(file, size, TRUE) :
  truncating string with embedded nuls
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Warning in readChar(file, size, TRUE) :
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Warning in readChar(file, size, TRUE) :
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Warning in readChar(file, size, TRUE) :
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Warning in readChar(file, size, TRUE) :
  truncating string with embedded nuls
Warning in readChar(file, size, TRUE) :
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Warning in readChar(file, size, TRUE) :
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data.rivm <- read_rds("../results/rivm.Rds") %>% rename(Rivm = Deaths)

Data for 2020 corona crisis

cols.corona <-

Warning messages:
1: In readChar(file, size, TRUE) : truncating string with embedded nuls
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3: In readChar(file, size, TRUE) : truncating string with embedded nuls
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  c(
    cols,
    "ExpectedMortality", "AvgMortality", "UnexpectedMortality", "ExcessiveMortality", "Flu2018"
  )

data.corona <- union_all(
  readRDS("../results/data.corona.Rds") %>% select(cols.corona),
  readRDS("../results/data.spatial.corona.Rds") %>% select(cols.corona, "RegioS") %>% mutate("Regio" = RegioS) %>% select(-RegioS)
) %>% 
  # left_join(data.flu2018, by = c("Period", "Regio")) %>%
  full_join(data.rivm, by = c("Regio", "Date")) %>%
  drop_na(Date)

Note: Using an external vector in selections is ambiguous.
i Use `all_of(cols.corona)` instead of `cols.corona` to silence this message.
i See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
This message is displayed once per session.

data.corona %>% filter(Regio == "NL")

Geographical entities

Warning in readChar(file, size, TRUE) :
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Warning in readChar(file, size, TRUE) :
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Warning in readChar(file, size, TRUE) :
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Warning in readChar(file, size, TRUE) :
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Warning in readChar(file, size, TRUE) :
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Warning in readChar(file, size, TRUE) :
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areas <- GET("https://opendata.arcgis.com/datasets/e1f0dd70abcb4fceabbc43412e43ad4b_0.geojson") %>% content(as = "text") %>%
  read_sf() %>%
  rename(RegioS = Gemeentecode) %>% 
  arrange(Gemeentenaam) 

No encoding supplied: defaulting to UTF-8.

write_rds(areas, "../results/plots/areas.Rds")

Create a timeline and add splines for smooth charts

data.mort

Warning messages:
1: In readChar(file, size, TRUE) : truncating string with embedded nuls
2: In readChar(file, size, TRUE) : truncating string with embedded nuls
3: In readChar(file, size, TRUE) : truncating string with embedded nuls
4: In readChar(file, size, TRUE) : truncating string with embedded nuls
5: In readChar(file, size, TRUE) : truncating string with embedded nuls
6: In readChar(file, size, TRUE) : truncating string with embedded nuls
7: In readChar(file, size, TRUE) : truncating string with embedded nuls
8: In readChar(file, size, TRUE) : truncating string with embedded nuls

Example 1

tooltip <- ("<b>{Date}</b>
Mortality rate: {floor(Value)}
{if(is.na(Absolute) "" else \"Deaths: {floor(Absolute)}\" %>% glue()}"

Error: unexpected string constant in:
"Mortality rate: {floor(Value)}
{if(is.na(Absolute) "" else \"Deaths: {floor(Absolute)}\" %>% glue()}""

Example 2

Spatial dataset

data.spatial_absolute <- areas %>% left_join(data.corona %>% filter(Interval == "month"), by = c("RegioS" = "Regio")) %>% 
    mutate(
      ActualMortality = round(MortalityRate * Population / 100000),
      ExpectedMortality = round(ExpectedMortality * Population / 100000),
      AvgMortality = round(AvgMortality * Population / 100000),
      UnexpectedMortality = round(UnexpectedMortality * Population / 100000),
      ExcessiveMortality = round(ExcessiveMortality * Population / 100000),
    ) 

write_rds(data.spatial_absolute, "../results/plots/spatial_absolute.Rds")

Example

Summary table